Move parmed to optional dependency

.travis.yml

@@ -86,6 +86,7 @@ matrix:
 #           SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"
 
     - env: NAME='minimal'
+           PIP_DEPENDENCIES=""
            CONDA_DEPENDENCIES=${CONDA_MIN_DEPENDENCIES}
            INSTALL_HOLE="false"
            CODECOV="true" SETUP_CMD="${PYTEST_FLAGS} --cov=MDAnalysis"

package/MDAnalysis/coordinates/ParmEd.py

@@ -162,9 +162,10 @@ def convert(self, obj):
         """
         try:
             import parmed as pmd
-        except ModuleNotFoundError:
-            raise ValueError('Parmed is required for ParmEdConverter but '
-                             'is not installed.')
+        except ImportError:
+            raise ImportError('ParmEd is required for ParmEdConverter but '
+                              'is not installed. Try installing it with \n'
+                              'pip install parmed')
         try:
             # make sure to use atoms (Issue 46)
             ag_or_ts = obj.atoms

package/MDAnalysis/core/_get_readers.py

@@ -65,7 +65,7 @@ def get_reader_for(filename, format=None):
       :class:`~MDAnalysis.coordinates.memory.MemoryReader` is returned.
     - If `filename` is an MMTF object,
       :class:`~MDAnalysis.coordinates.MMTF.MMTFReader` is returned.
-    - If `filename` is a ParmEd Structure, 
+    - If `filename` is a ParmEd Structure,
       :class:`~MDAnalysis.coordinates.ParmEd.ParmEdReader` is returned.
     - If `filename` is an iterable of filenames,
       :class:`~MDAnalysis.coordinates.chain.ChainReader` is returned.
@@ -176,7 +176,7 @@ def get_writer_for(filename, format=None, multiframe=None):
                 None)
         else:
             format = util.check_compressed_format(root, ext)
-    
+
     if format == '':
         raise ValueError((
             'File format could not be guessed from {}, '
@@ -275,7 +275,7 @@ def get_converter_for(format):
     TypeError
         If no appropriate parser could be found.
 
-    
+
     .. versionadded:: 0.21.0
     """
     try:

package/setup.py

@@ -558,7 +558,6 @@ def dynamic_author_list():
           'scipy>=1.0.0',
           'matplotlib>=1.5.1',
           'mock',
-          'parmed',
     ]
     if not os.name == 'nt':
         install_requires.append('gsd>=1.4.0')
@@ -593,7 +592,7 @@ def dynamic_author_list():
           ext_modules=exts,
           requires=['numpy (>=1.13.3)', 'biopython (>= 1.71)', 'mmtf (>=1.0.0)',
                     'networkx (>=1.0)', 'GridDataFormats (>=0.3.2)', 'joblib',
-                    'scipy (>=1.0.0)', 'matplotlib (>=1.5.1)', 'parmed'],
+                    'scipy (>=1.0.0)', 'matplotlib (>=1.5.1)'],
           # all standard requirements are available through PyPi and
           # typically can be installed without difficulties through setuptools
           setup_requires=[

testsuite/MDAnalysisTests/coordinates/test_parmed.py

@@ -23,7 +23,6 @@
 from __future__ import absolute_import
 
 import pytest
-import parmed as pmd
 import MDAnalysis as mda
 
 from numpy.testing import (assert_equal,
@@ -45,6 +44,9 @@
     PRM_UreyBradley,
 )
 
+pmd = pytest.importorskip('parmed')
+
+
 class TestParmEdReaderGRO:
     ref_filename = GRO
 
@@ -67,7 +69,6 @@ def test_coordinates(self):
 
 
 class BaseTestParmEdReader(_SingleFrameReader):
-
     def setUp(self):
         self.universe = mda.Universe(pmd.load_file(self.ref_filename))
         self.ref = mda.Universe(self.ref_filename)

testsuite/MDAnalysisTests/topology/test_parmed.py

@@ -23,7 +23,6 @@
 from __future__ import absolute_import
 
 import pytest
-import parmed as pmd
 import MDAnalysis as mda
 
 from MDAnalysisTests.topology.base import ParserBase
@@ -32,6 +31,8 @@
     PRM
 )
 
+pmd = pytest.importorskip('parmed')
+
 class BaseTestParmedParser(ParserBase):
     parser = mda.topology.ParmEdParser.ParmEdParser
     expected_attrs = ['ids', 'names', 'types', 'masses',
@@ -62,6 +63,10 @@ def filename(self):
     def universe(self, filename):
         return mda.Universe(filename)
 
+    def test_creates_universe(self, filename):
+        u = mda.Universe(filename)
+        assert isinstance(u, mda.Universe)
+
     def test_bonds_total_counts(self, top, filename):
         unique = set([(a.atom1.idx, a.atom2.idx)
                       for a in filename.bonds])
@@ -236,4 +241,3 @@ def test_dihedral_types(self, universe):
         )):
             assert dih.type[i].type.phi_k == phi_k
             assert dih.type[i].type.per == per
-